UW’s Protein Guru, David Baker, Eyes Alternative Biofuels, Vaccines in New 3-D Structures

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in a paper in Science, that it could create a protein that didn’t exist in nature. It won an award for the best paper in that leading scientific journal that year, he says.

Protein structure might sound hopelessly theoretical to the man on the street, but Baker has worked for years to engage the public in this science. The most visible way has been through [email protected]. This is the distributed computing project that emerged from beta mode in October 2005, in which people around the world download some software that uses their computer to run calculations when it’s not in normal use.

The fruits of this labor are provided free to academic and nonprofit researchers, and cost a $35,000 license fee to companies. Baker—in keeping with what Grabs said about not wanting to become rich—takes the license income and uses it for an all-expenses paid annual retreat for the former students and other academic developers who work on the project at Sleeping Lady Mountain Retreat near Leavenworth, WA (selected for its many great hiking trails nearby).

As the power of the computers to characterize proteins has grown, Baker has gravitated toward the next challenge of creating new proteins and enzymes for all sorts of industrial purposes. The first protein created in 2003 didn’t really do anything, Baker says. Since then, the lab has gotten better at it, creating more than 60 different enzymes using the technique, and had its work published in further articles in Science and Nature, which has grabbed the attention of more than a few industrial biotech companies.

Last year, several companies approached Baker, offering to sponsor particular projects of theirs in his lab. He had to say no, because his funding from the Howard Hughes Medical Institute stipulates that he stick to basic research, and not do applied work for companies. That prompted three members of his lab—Eric Althoff, Alexandre Zanghellini, and Grabs—to get Arzeda established. They’ve recently won committed venture financing from OVP Venture Partners and WRF Capital.

Baker has a limited role as a scientific advisor to the company, but he says he doesn’t have entrepreneurial dreams of his own. He says he’s excited about the potential for applications, and that it provides another career path for his students and postdocs, as an alternative to faculty jobs at a university.

As for his management style, Baker likes to walk around the lab, which is a relatively big academic group of about 40 people. He says he tries to talk to people in the lab every day. Unlike a lot of faculty, he avoids travel, heading to the East Coast only once a year to deliver a series of talks on his work. “My job is here to push the research along. I travel much less than most people. I’ve heard myself talk before,” he says.

So what makes him stand out? Parekh, the CEO of Bio Architecture Lab, says Baker is “very competitive and drives people in his lab to achieve excellence.” Althoff adds that Baker is open to new ideas, and is collaborative in the academic community. “He shares his results publicly very early on in order to get people outside of his lab’s opinions and thoughts on how to best go forward,” Althoff says. “He continually insists on using the best control experiments to verify that results are real.”

Baker relished talking about applications during our conversation, particularly ones with broad societal implications—like vaccines for HIV, or a genetically modified banana that might protect people from getting sick with cholera. But when I asked about where all this work is headed, and what his ultimate goals are, he chose not to get carried away with a promise that he might not be able to deliver, or that is at least decades away.

“We can’t predict protein structures perfectly now,” Baker says. “We’d like to design active catalysts, proteins that bind tightly to other proteins, drugs useful for diseases, vaccines that work. A lot of problems we work on are really hard. For the short-term, it’s really about being better at what we’re doing than we are now.”

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One response to “UW’s Protein Guru, David Baker, Eyes Alternative Biofuels, Vaccines in New 3-D Structures”

  1. Chad WaiteChad Waite says:

    About time some one wrote about the awesome work that David is doing.
    We are excited about starting a company with soem of David’s followers.